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haplotype analysis

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https://www.readbyqxmd.com/read/29240829/celsr2-is-a-candidate-susceptibility-gene-in-idiopathic-scoliosis
#1
Elisabet Einarsdottir, Anna Grauers, Jingwen Wang, Hong Jiao, Stefan A Escher, Aina Danielsson, Ane Simony, Mikkel Andersen, Steen Bach Christensen, Kristina Åkesson, Ikuyo Kou, Anas M Khanshour, Acke Ohlin, Carol Wise, Shiro Ikegawa, Juha Kere, Paul Gerdhem
A Swedish pedigree with an autosomal dominant inheritance of idiopathic scoliosis was initially studied by genetic linkage analysis, prioritising genomic regions for further analysis. This revealed a locus on chromosome 1 with a putative risk haplotype shared by all affected individuals. Two affected individuals were subsequently exome-sequenced, identifying a rare, non-synonymous variant in the CELSR2 gene. This variant is rs141489111, a c.G6859A change in exon 21 (NM_001408), leading to a predicted p.V2287I (NP_001399...
2017: PloS One
https://www.readbyqxmd.com/read/29232306/differential-effect-of-abcb1-haplotypes-on-promoter-activity
#2
Jordan T Speidel, Meixiang Xu, Sherif Z Abdel-Rahman
OBJECTIVE: Promoter single-nucleotide polymorphisms (SNPs) of the ABCB1 gene, encoding the placental efflux transporter P-glycoprotein, can affect its expression and alter xenobiotic transfer from the maternal to the fetal circulation. Because SNPs are arranged in specific combinations as defined haplotypes, the aims of this study were to: (i) determine the placental haplotype structure of the ABCB1 promoter and (ii) determine the differential effect of these haplotypes on placental ABCB1 promoter activity...
December 11, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/29230376/population-structure-and-phenotypic-variation-of-sclerotinia-sclerotiorum-from-dry-bean-phaseolus-vulgaris-in-the-united-states
#3
Zhian N Kamvar, B Sajeewa Amaradasa, Rachana Jhala, Serena McCoy, James R Steadman, Sydney E Everhart
The ascomycete pathogen Sclerotinia sclerotiorum is a necrotrophic pathogen on over 400 known host plants, and is the causal agent of white mold on dry bean. Currently, there are no known cultivars of dry bean with complete resistance to white mold. For more than 20 years, bean breeders have been using white mold screening nurseries (wmn) with natural populations of S. sclerotiorum to screen new cultivars for resistance. It is thus important to know if the genetic diversity in populations of S. sclerotiorum within these nurseries (a) reflect the genetic diversity of the populations in the surrounding region and (b) are stable over time...
2017: PeerJ
https://www.readbyqxmd.com/read/29230063/multiple-gene-genealogy-reveals-high-genetic-diversity-and-evidence-for-multiple-origins-of-chinese-plasmopara-viticola-population
#4
Wei Zhang, Ishara S Manawasinghe, Wensheng Zhao, Jianping Xu, Siraprapa Brooks, Xueyan Zhao, Kevin D Hyde, K W Thilini Chethana, Jianhua Liu, Xinghong Li, Jiye Yan
Downy mildew caused by Plasmopara viticola is one of the most devastating diseases of grapevines worldwide. So far, the genetic diversity and origin of the Chinese P. viticola population are unclear. In the present study, 103 P. viticola isolates were sequenced at four gene regions: internal transcribed spacer one (ITS), large subunit of ribosomal RNA (LSU), actin gene (ACT) and beta-tubulin (TUB). The sequences were analyzed to obtain polymorphism and diversity information of the Chinese population as well as to infer the relationships between Chinese and American isolates...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229810/disease-onset-in-x-linked-dystonia-parkinsonism-correlates-with-expansion-of-a-hexameric-repeat-within-an-sva-retrotransposon-in-taf1
#5
D Cristopher Bragg, Kotchaphorn Mangkalaphiban, Christine A Vaine, Nichita J Kulkarni, David Shin, Rachita Yadav, Jyotsna Dhakal, Mai-Linh Ton, Anne Cheng, Christopher T Russo, Mark Ang, Patrick Acuña, Criscely Go, Taylor N Franceour, Trisha Multhaupt-Buell, Naoto Ito, Ulrich Müller, William T Hendriks, Xandra O Breakefield, Nutan Sharma, Laurie J Ozelius
X-linked dystonia-parkinsonism (XDP) is a neurodegenerative disease associated with an antisense insertion of a SINE-VNTR-Alu (SVA)-type retrotransposon within an intron of TAF1 This unique insertion coincides with six additional noncoding sequence changes in TAF1, the gene that encodes TATA-binding protein-associated factor-1, which appear to be inherited together as an identical haplotype in all reported cases. Here we examined the sequence of this SVA in XDP patients (n = 140) and detected polymorphic variation in the length of a hexanucleotide repeat domain, (CCCTCT)n The number of repeats in these cases ranged from 35 to 52 and showed a highly significant inverse correlation with age at disease onset...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229744/three-reportedly-unrelated-families-with-liddle-syndrome-inherited-from-a-common-ancestor
#6
Luca Pagani, Yoan Diekmann, Marco Sazzini, Sara De Fanti, Maurizio Rondinelli, Enrico Farnetti, Bruno Casali, Amelia Caretto, Francesca Novara, Orsetta Zuffardi, Paolo Garagnani, Franco Mantero, Mark G Thomas, Donata Luiselli, Ermanno Rossi
Liddle syndrome is considered a rare Mendelian hypertension. We have previously described 3 reportedly unrelated families, native of an Italian area around the Strait of Messina, carrying the same mutation (βP617L) of the epithelial sodium channel. The aims of our study were (1) to evaluate whether a close genomic relationship exists between the 3 families through the analysis of mitochondrial DNA and Y chromosome; and (2) to quantify the genomic relatedness between the patients with Liddle syndrome belonging to the 3 families and assess the hypothesis of a mutation shared through identity by descent...
December 11, 2017: Hypertension
https://www.readbyqxmd.com/read/29228700/association-of-ifngr1-and-ifng-genetic-polymorphisms-with-the-risk-for-pulmonary-tuberculosis-in-the-chinese-tibetan-population
#7
Shumei He, Bo Wang, Xikai Zhu, Zhengshuai Chen, Junyu Chen, Demi Hua, Deji Droma, Wensheng Li, Dongya Yuan, Tianbo Jin
Interferon-gamma (IFNG) and its receptor (IFNGR1) are principal genes that associated with tuberculosis. In the current study we aimed to explore the genetic association of polymorphisms of IFNG and IFNGR1 with the risk of pulmonary tuberculosis (PTB) in the Chinese Tibetan population. We selected 467 PTB patients and 503 healthy controls to genotype 9 single nucleotide polymorphisms (SNPs). The unconditional logistic regression analysis was applied for assessing the associations, and the risk of PTB were evaluated by calculating the odds ratio (OR) and 95% confidence interval (CI)...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228205/associations-between-polymorphisms-in-genes-related-to-estrogen-metabolism-and-function-and-prostate-cancer-risk-results-from-the-prostate-cancer-prevention-trial
#8
Li Tang, Mary E Platek, Song Yao, Cathee Till, Phyllis J Goodman, Catherine M Tangen, Yue Wu, Elizabeth A Platz, Marian L Neuhouser, Frank Z Stanczyk, Juergen K V Reichardt, Regina M Santella, Ann Hsing, William D Figg, Scott M Lippman, Ian M Thompson, Christine B Ambrosone
Substantial preclinical data suggest estrogen's carcinogenic role in prostate cancer development; however, epidemiological evidence based on circulating estrogen levels is largely null. Compared with circulating estrogen, the intraprostatic estrogen milieu may play a more important role in prostate carcinogenesis. Using a nested case-control design in the Prostate Cancer Prevention Trial (PCPT), we examined associations of genetic variants of genes that are involved in estrogen synthesis, metabolism and function with prostate cancer risk...
December 8, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/29227583/single-point-mutation-on-the-gene-encoding-dysbindin-results-in-recognition-deficits
#9
Eric H Chang, Kayla Fernando, Lok Wan E Yeung, Kristina Barbari, Toni-Shay S Chandon, Anil K Malhotra
The dystrobrevin-binding protein 1 (DTNBP1) gene is a candidate risk factor for schizophrenia and has been associated with cognitive ability in both patient populations and healthy controls. DTNBP1 encodes dysbindin protein, which is localized to synaptic sites and is reduced in the prefrontal cortex and hippocampus of patients with schizophrenia, indicating a potential role in schizophrenia etiology. Most studies of dysbindin function have focused on the sandy (sdy) mice that lack dysbindin protein and have a wide range of abnormalities...
December 11, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29226035/molecular-evolution-of-virulence-genes-and-non-virulence-genes-in-clinical-natural-and-artificial-environmental-legionella-pneumophila-isolates
#10
Xiao-Yong Zhan, Qing-Yi Zhu
Background: L. pneumophila is the main causative agent of Legionnaires' disease. Free-living amoeba in natural aquatic environments is the reservoir and shelter for L. pneumophila. From natural water sources, L. pneumophila can colonize artificial environments such as cooling towers and hot-water systems, and then spread in aerosols, infecting the susceptible person. Therefore, molecular phylogeny and genetic variability of L. pneumophila from different sources (natural water, artificial water, and human lung tissue) might be distinct because of the selection pressure in different environments...
2017: PeerJ
https://www.readbyqxmd.com/read/29225355/evolutionary-conservation-and-functional-divergence-of-the-lfk-gene-family-play-important-roles-in-the-photoperiodic-flowering-pathway-of-land-plants
#11
Ling Lu, Yuanqi Wu, Zhengqiao Liao, Jing Xiong, Fengkai Wu, Jie Xu, Hai Lan, Qiling Tang, Shufeng Zhou, Yaxi Liu, Yanli Lu
ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1)-blue-light photoreceptors-play important roles in regulating the circadian clock and photoperiodic flowering pathway in plants. In this study, phylogenetic analysis revealed that the LOV (Light, Oxygen, or Voltage) and Kelch repeat-containing F-box (LFK) gene family can be classified into two clades, ZTL/LKP2 and FKF1, with clear differentiation between monocots and dicots within each clade. The LFK family genes underwent strong purifying selection; however, signatures of positive selection to adapt to local conditions still existed in 18 specific codons...
December 11, 2017: Heredity
https://www.readbyqxmd.com/read/29224405/phylogeography-and-genetic-population-structure-of-the-spadenose-shark-scoliodon-macrorhynchos-from-the-chinese-coast
#12
Xiao Chen, Jun-Jie Wang, Wei-Ming Ai, Hao Chen, Hung-Du Lin
The population structure of Scoliodon macrorhynchos from the Chinese coast was investigated using the mitochondrial control region. All 19 mtDNA haplotypes from 219 sequences were identified. Relatively high average haplotype diversity (0.797) and relatively low average nucleotide diversity (0.0013) were found together with a recent and sudden population expansion. Analysis of the mismatch distributions, neutrality tests and Bayesian skyline plot showed a pattern consistent with a recent population expansion event that may have taken place during the last glacial maximum (LGM)...
December 11, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/29222496/genome-wide-and-gene-based-association-mapping-for-rice-eating-and-cooking-characteristics-and-protein-content
#13
Xiaoqian Wang, Yunlong Pang, Jian Zhang, Zhichao Wu, Kai Chen, Jauhar Ali, Guoyou Ye, Jianlong Xu, Zhikang Li
Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222432/genetic-variants-of-the-receptor-for-advanced-glycation-end-products-in-susceptibility-to-type-2-diabetes-mellitus-in-primary-hypertensive-patients
#14
Hualing Yang, Yangyang Nie, Zhenyi Chen, Linyang Ye, Qingxiang Wang, Zhanxiang Wang
Diabetes mellitus is frequently comorbid with hypertension, which is approximately twice as common as diabetes mellitus in China. We designed a case-control association study to inspect the susceptibility of the receptor for advanced glycation end-products (RAGE) gene 6 variants to type 2 diabetes mellitus (T2DM) in 2199 patients with primary hypertension (1252 diabetic cases and 947 nondiabetic controls). The genotypes/alleles of -429T > C and 82Gly > Ser variants differed significantly between the two groups, and their associations with T2DM were significant after Bonferroni correction...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221994/allele-and-haplotype-diversity-of-12-x-strs-in-sardinia
#15
C Robino, D Lacerenza, S Aneli, C Di Gaetano, G Matullo, R Robledo, C Calò
The analysis of clusters of tightly linked X-chromosome short tandem repeat (STR) markers can assist the interpretation of complex kinship cases. However, when linkage disequilibrium (LD) is present in the population of origin of tested individuals, haplotype rather than allele frequencies should be used in likelihood calculations. The diversity of twelve X-STRs arranged in four linkage groups (I: DXS10148-DXS10135-DXS8378; II: DXS7132-DXS10079-DXS10074; III: DXS10103-HPRTB-DXS10101; IV: DXS10146-DXS10134-DXS7423) was tested in a Sardinian population sample (n=516) including three open populations from the Northern, Central and Southern part of the island, and three isolates (Benetutti, Desulo, Carloforte)...
December 5, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29221201/functional-fgfr4-gly388arg-polymorphism-contributes-to-oral-squamous-cell-carcinoma-susceptibility
#16
Chia-Hsuan Chou, Ming-Ju Hsieh, Chun-Yi Chuang, Jen-Tsun Lin, Chia-Ming Yeh, Pao-Yu Tseng, Shun-Fa Yang, Mu-Kuan Chen, Chiao-Wen Lin
Aberrations of the fibroblast growth factor receptor 4 (FGFR4) genomic region include amplification of FGFR4, activation of FGFR4 kinase domain mutations, and overexpression of FGFR4, which lead to sustained cell proliferation and contribute to tumor development. However, the association between FGFR4 single-nucleotide polymorphisms (SNPs) and risk of oral squamous cell carcinoma (OSCC) remains to be determined. We investigated the relationships between FGFR4 genetic polymorphisms, OSCC development and clinicopathological variables...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221136/kif3a-and-il-4-are-disease-specific-biomarkers-for-psoriatic-arthritis-susceptibility
#17
Raffaella Cascella, Claudia Strafella, Michele Ragazzo, Laura Manzo, Gaetana Costanza, John Bowes, Ulrike Hüffmeier, Saverio Potenza, Federica Sangiuolo, André Reis, Anne Barton, Giuseppe Novelli, Augusto Orlandi, Emiliano Giardina
To date, the genes associated with Psoriatic Arthritis (PsA) are principally involved in inflammation, immune response and epidermal differentiation, without any information about the relationship between disease and bone metabolism genes. Our work was focused on 5q31 locus, which contains several genetic variants significantly associated with PsA. The study involved 1526 subjects (500 PsA, 426 PsV, 600 controls). The region was evaluated by selecting and genotyping the SNPs of interest by Real Time PCR and direct sequencing...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220824/extensive-geographical-and-social-structure-in-the-paternal-lineages-of-saudi-arabia-revealed-by-analysis-of-27-y-strs
#18
Yahya M Khubrani, Jon H Wetton, Mark A Jobling
Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74...
December 2, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29220419/high-resolution-single-cell-sequencing-of-malaria-parasites
#19
Simon G Trevino, Standwell C Nkhoma, Shalini Nair, Benjamin J Daniel, Karla Moncada, Stanley Khoswe, Rachel L Banda, François Nosten, Ian H Cheeseman
Single-cell genomics is a powerful tool for determining the genetic architecture of complex communities of unicellular organisms. In areas of high transmission, malaria patients are often challenged by the activities of multiple Plasmodium falciparum lineages, which can potentiate pathology, spread drug resistance loci and also complicate most genetic analysis. Single-cell sequencing of P. falciparum would be key to understanding infection complexity, though efforts are hampered by the extreme nucleotide composition of its genome (∼80% AT-rich)...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29220389/association-of-genetic-variations-in-foxo3-gene-with-susceptibility-to-noise-induced-hearing-loss-in-a-chinese-population
#20
Haoran Guo, Enmin Ding, Ying Bai, Hengdong Zhang, Huanxi Shen, Jun Wang, Xianping Song, Wenyan Cai, Jiadi Guo, Baoli Zhu
Noise induced hearing loss (NIHL), a multifactorial disease involving both genetic and environmental factors, is one of the most important occupational health hazards. Nonetheless, the influence of FOXO3 variants on NIHL risk have not been illuminated. This research was conducted to explore the effects of FOXO3 polymorphisms on individual susceptibility to NIHL. A total of 2689 industrial workers from one textile factory of east China were recruited to participate in the current research. Venous blood was collected, questionnaire and pure-tone audiometry (PTA) was conducted by specialist physicians...
2017: PloS One
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